Viral recombination occurs when viruses of two different parent strains coinfect the same host cell and interact during replication to generate virus progeny that have some genes from both parents. Recombination generally occurs between members of the same virus type (e.g., between two influenza viruses or between two herpes simplex viruses). Two mechanisms of recombination have been observed for viruses: independent assortment and incomplete linkage. Either mechanism can produce new viral serotypes or viruses with altered virulence.
After infection of a cell with two viruses with two or more genetic segments (“chromosomes”), reassortment of the replicated segments can occur. Independent assortment results in the generation of progeny viruses whose genomes contain segments of genome from both types of parental viruses.
). These genes are unlinked and assort at random. Recombination by independent assortment has been reported, for example, for the influenza viruses and other orthomyxoviruses (8 segments of single-stranded RNA) and for the reoviruses (10 segments of double-stranded RNA). The frequency of recombination by independent assortment is 6 to 20 percent for orthomyxoviruses. Independent assortment between an animal and a human strain of influenza virus (see Ch. 58) during a mixed infection can yield an antigenically novel influenza virus strain capable of infecting humans but carrying animal-strain hemagglutinin and/or neuraminidase surface molecules. This recombinant can infect individuals that are immune to the parent human virus. This mechanism results in an immediate, major antigenic change and is called antigenic shift. Antigenic shifts in influenza virus antigens can give rise to pandemics (worldwide epidemics) of influenza. Such antigenic shifts have occurred relatively frequently during recent history (Table 43-2). Because the number of different serotypes of hemagglutinin and neuraminidase are limited, a given strain reappears from time to time. For example, the H1N1 influenza virus strain was responsible for the 1918 to 1919 influenza pandemic that caused 20 million deaths. The same virus also caused pandemics in 1934 and in 1947, then disappeared after 1958 and reappeared in 1977. The reappearance of virus strains after an absence is believed to be the result of recombinational events involving the independent assortment of genes from two variant viruses.
. The genetic interaction of DNA viruses can result in break-rejoin recombination, in which the two DNA molecules of different viruses break and then cross over. Break-rejoin recombination results in novel progeny viruses with some DNA sequences of both types of parental viruses.
). Genes that generally segregate together are called linked genes. If recombination occurs between them, the linkage is said to be incomplete. Recombination of incompletely linked genes occurs in all DNA viruses that have been studied and in several RNA viruses.
). The severed DNA strands are then rejoined to the DNA strands of a different DNA molecule that has been broken in a similar site. Recombination rates for herpesviruses, which are DNA viruses that replicate in the nucleus of infected cells, approximate those expected for a eukaryotic genome of the size of the herpesvirus genome. Herpesviruses have an average recombination frequency of 10 to 20 percent for any two loci. However, the rate of recombination between a specific pair of genetic loci depends on the distance between them and varies from less than 1 percent to approximately 50 percent. Measurement of the recombination frequencies for different loci can be used to map the virus genome. In this type of genetic map, loci with high recombination frequencies are far apart and loci with low recombination frequencies are close together.
Recombination has been shown to occur in several positive-sense single-stranded RNA virus groups: retroviruses, picornaviruses, and coronaviruses. That is initially surprising, as recombination between RNA molecules has not been observed in prokaryotic or eukaryotic cells. In retroviruses, recombination actually occurs at the point in replication when the retrovirus genome is in a DNA form and takes place by the same break-rejoin mechanism as in cells and DNA viruses. Recombination can occur both between two related retroviruses and between the retrovirus DNA and the host cell DNA. Recombination between two retroviruses gives rise to novel viral progeny with reassorted genes. Recombination between retroviruses and the host cell can give rise to novel viral progeny that carry nonviral genes. If these host genes code for growth factors, growth factor receptors, or a number of other specific cellular proteins, the recombinant retroviruses may be oncogenic (see Ch. 47).
In this mechanism, the polymerase begins replicating RNA template. By an unknown mechanism, which may involve a high degree of secondary structure in the viral RNA template, the polymerase complex (with its nascent viral RNA molecule) reassociates with the template viral RNA of different parental virus, such that the nascent RNA molecule will be synthesized as a novel recombinant virus whose RNA genome contains genes from each parental virus type.
). Copy-choice may occur in these RNA viruses because the viral RNA polymerase binds to only a few bases of the template RNA at any one time. Such a weak interaction of the polymerase with the template RNA would permit the polymerase, carrying its RNA strand, to disassociate from the original template nucleic acid strand and then associate with a new template RNA strand. Recombination frequencies in the range of 0.2 to 0.4 percent have been reported. Therefore, the efficiency of this mechanism of recombination is low.
As mentioned above, viral recombination is important because it can generate novel progeny viruses that express new antigenic and/or virulence characteristics. For example, the novel progeny viruses may have new surface proteins that permit them to infect previously resistant individuals; they may have altered virulence characteristics; they may have novel combinations of proteins that make them infective to new cells in the original host or to new hosts; or they may carry material of cellular origin that gives them oncogenic potential.
Vaccinia virus genomic DNA is cut with an endonuclease. A specific sequence of DNA (with appropriate regulatory sequences) coding for a protein (e.g., cholera toxin) to be used as an immunogen is ligated into the vaccinia virus genome, making a recombinant vaccinia virus. The DNA will be transcribed and the immunogen will be produced along with vaccinia virus proteins in infected cells following vaccination. The immunogen will then elicit antibody production by the host, providing protective immunity.
). For example, vaccinia virus strains carrying DNA coding for bacterial and viral antigens have been produced. It is expected that after vaccination with the recombinant vaccinia virus, the bacterial or viral antigen (immunogen) will be produced. The presence of this immunogen will then stimulate specific antibody production by the host, resulting in protection of the host from the immunogen. Studies with these live, recombinant vaccinia viruses are currently under way to determine whether inoculation of the skin with the recombinant virus can induce a protective host antibody response to the bacterial or viral antigens. Other studies are investigating the use of live, recombinant adenoviruses containing bacterial or viral genes to infect the gastrointestinal tract and induce both mucosal and systemic immunity.
In a similar manner, recombinant viruses are also being developed that carry normal human genes. It is envisioned that such recombinant viruses could be useful for gene therapy. Target diseases for gene therapy span a wide range, including diabetes, cystic fibrosis, severe combined immunodeficiency syndrome, etc. Indeed, treatment of cystic fibrosis patients with replication deficient, recombinant adenoviruses bearing a normal copy of the cystic fibrosis transmembrane regulator gene has already been approved.
If these studies give positive results, such directed generation of recombinant viruses may become an important tool in the development of vaccines and for gene therapy.
